I gather that GE would replace the part under warranty but you need to pay labor? $200 to replace a magnetron seems way out of line just for labor.
The magnetron is the most likely part to cause your symptom. Capacitors and diodes usually fail by shorting, and cause the oven to make loud humming noises or blow the fuse. But the trouble might also be due to the control circuit board, either bad parts or solder connections.
Unless you have the proper tools and experience, trying to diagnose where the trouble is can be very hazardous. There are lethal voltages present with the cover off and the oven operating. You should leave the repair to a professional. An independent shop might be able to diagnose the problem and give you an estimate for a lower charge, and then you could decide whether to repair or replace.
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